Mammalian CDP-diacylglycerol synthase

ABSTRACT

There is disclosed cDNA sequences and polypeptides having the enzyme CDP-diacylglycerol synthase (CDS) activity. CDS is also known as CTP:phosphatidate cytidylyltransferase. There is further disclosed methods for isolation and production of polypeptides involved in phosphatidic acid metabolism and signaling in mammalian cells, in particular, the production of purified forms of CDS.

TECHNICAL FIELD OF THE INVENTION

This present invention provides cDNA sequences and polypeptides having the enzyme CDP-diacylglycerol synthase (CDS) activity. CDS is also known as CTP:phosphatidate cytidyltransferase (EC2.7.7.41). The present invention further provides for isolation and production of polypeptides involved in phosphatidic acid metabolism and signaling in mammalian cells, in particular, the production of purified forms of CDS.

BACKGROUND OF THE INVENTION

CDP-diacylglycerol (DAG) is an important branch point intermediate just downstream of phosphatidic acid (PA) in the pathways for biosynthesis of glycerophosphate-based phospholipids (Kent, Anal. Rev. Biochem. 64: 315-343, 1995). In eukaryotic cells, PA, the precursor molecule for all glycerophospholipid, is converted either to CDP-DAG by CDP-DAG synthase (CDS) or to DAG by a phosphohydrolase. In mammalian cells, CDP-DAG is the precursor to phosphatidylinositol (PI), phosphatidylglycerol (PG), and cardiolipin (CL). Diacylglycerol is the precursor to triacylglycerol, phosphatidylethanolamine, and phosphatidylcholine in eukaryotic cells. Therefore, the partitioning of phosphatidic acid between CDP-diacylglycerol and diacylglycerol must be an important regulatory point in eukaryotic phospholipid metabolism (Shen et al., J. Biol. Chem. 271: 789-795, 1996). In eukaryotic cells, CDP-diacylglycerol is required in the mitochondria for phosphatidylglycerol and cardiolipin synthesis and in the endoplasmic reticulum and possibly other organelles for the synthesis of phosphatidylinositol (PI). PI, in turn, is the precursor for the synthesis of a series of lipid second messengers, such as phosphatidylinositol-4,5-bisphosphate (PIP₂), DAG and inositol-1,4,5-trisphosphate (IP₃). Specifically, PIP₂ is the substrate for phospholipase C that is activated in response to a wide variety of extracellular stimuli, leading to the generation of two lipid second messengers; namely, DAG for the activation of protein kinase C and IP₃ for the release of Ca⁺⁺ from internal stores (Dowhan, Anal. Rev. Biochem. 66: 199-232, 1997).

The genes coding for CDS have been identified in E. coli (Icho et al, J. Biol. Chem. 260: 12078-12083, 1985), in yeast (Shen et al., J. Biol. Chem. 271: 789-795, 1996), and in Drosophila (Wu et al., Nature 373: 216-222, 1995). A human cDNA coding for CDS (hCDS1) is described by us herein and has been reported in Weeks et al., DNA Cell Biol. 16: 281-289, 1997. Moreover, Heacock et al., J. Neurochem. 67: 2200-2203, 1997 report cloning of a CDS 1 from a human neuronal cell line. Furthermore, Lykidis et al., J. Biol. Chem 272: 334102-33409, 1997 and Halford et al., Genomics 54: 140-144, 1998 both report DNA sequences suspected to encode a human cds2 protein, but these references fail to disclose either biological activity or an intact N-terminal region for the putative proteins.

It is of interest to isolate polynucleotides coding for human CDS and express them in mammalian cells to determine the potential roles of this enzyme in cellular function and use this enzyme as a target for the development of specific compounds that are modulators of its activity. With the advance in the understanding of disease processes, it has been found that many diseases result from the malfunction of intracellular signaling. This recognition has led to research and development of therapies based on the interception of signaling pathways in diseases (Levitzki, Curr. Opin. Cell Biol. 8: 239-244, 1996). Compounds that modulate CDS activity, and hence modulate generation of a variety of lipid second messengers and signals involved in cell activation, are therefore of therapeutic interest generally, and of particular interest in the areas of inflammation and oncology.

SUMMARY OF THE INVENTION

The present invention provides cDNA sequences, polypeptide sequences, and transformed cells for producing isolated recombinant mammalian CDS. The present invention provides two novel human polypeptides and fragment thereof, having CDS activity. The polypeptides discovered herein are novel and will be called hCDS1 (human CDS1) and hCDS2 (human CDS2). CDS catalyzes the conversion of phosphatidic acid (PA) to CDP-diacylglycerol (CDP-DAG), which in turn is the precursor to phosphatidylinositol (PI), phosphatidylglycerol (PG) and cardiolipin (CL).

The present invention further provides nucleic acid sequences coding for expression of the novel CDS polypeptides and active fragments thereof. The invention further provides purified CDS mRNAs and antisense oligonucleotides for modulation of expression of the genes coding for CDS polypeptides. Assays for screening test compounds for their ability to modulate CDS activity are also provided.

Recombinant CDS is useful for screening candidate drug compounds that modulate CDS activity, particularly those compounds that activate or inhibit CDS activity. The present invention provides cDNA sequences encoding a polypeptide having CDS activity and comprising the DNA sequence set forth in SEQ ID NO. 1 (hCDS1), the DNA sequence set forth in FIG. 8 (hCDS2), shortened fragments thereof, or additional cDNA sequences which due to the degeneracy of the genetic code encode a polypeptide of SEQ ID NO. 2 (hCDS1), a polypeptide of FIG. 8 (hCDS2), or biologically active fragments thereof, or a sequence hybridizing thereto under high stringency conditions. The present invention further provides a polypeptide having CDS activity and comprising the amino acid sequence of SEQ ID NO. 2 (hCDS1), the amino acid sequence of FIG. 8 (hCDS2), or biologically active fragments thereof.

Also provided by the present invention are vectors containing a DNA sequence encoding a mammalian CDS enzyme in operative association with an expression control sequence. Host cells, transformed with such vectors for use in producing recombinant CDS are also provided with the present invention. The inventive vectors and transformed cells are employed in a process for producing recombinant mammalian CDS. In this process, a cell line transformed with a cDNA sequence encoding a CDS enzyme in operative association with an expression control sequence, is cultured. The claimed process may employ a number of known cells as host cells for expression of the CDS polypeptide, including, for example, mammalian cells, yeast cells, insect cells and bacterial cells.

Another aspect of this invention provides a method for identifying a pharmaceutically-active compound by determining if a selected compound modulates the activity of CDS for converting PA to CDP-DAG. A compound having such activity is capable of modulating signaling kinase pathways and being a pharmaceutical compound useful for augmenting trilineage hematopoiesis after cytoreductive therapy and for anti-inflammatory activity in inhibiting the inflammatory cascade following hypoxia and reoxygenation injury (e.g., sepsis, trauma, ARDS, etc.).

The present invention further provides a transformed cell that expresses active mammalian CDS and further comprises a means for determining if a drug candidate compound is therapeutically active by modulating recombinant CDS activity.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the cDNA sequence encoding hCDS1. The nucleotide sequence analysis and restriction mapping of the cDNA clone revealed a 5′-untranslated region of 149 base pairs, an open reading frame capable of encoding a 461 amino acid polypeptide that spans nucleotide positions 150 to 1535 and a 3′-untranslated region of 520 base pairs.

FIG. 2 shows the translated amino acid sequence of hCDS1.

FIG. 3 shows the amino acid sequence of hCDS1.

FIG. 4 shows the sequence homology among the hCDS1 coding sequence, the yeast CDS coding sequence, E. coli CDS coding sequence, and the Drosophila CDS coding sequence. This comparison shows that hCDS1 has the greatest extended homology with amino acids 109 to 448 of Drosophila CDS. The hCDS1 protein and the CDS protein from Drosophila, yeast, and E. coli have 45%, 21% and 7% overall match in amino acid sequence, respectively.

FIG. 5 shows the results of in vitro hCDS1 activity assays on cell fractions from stable transfectants of NCI-H460 cells. CDS activity was assessed by conversion of (α-³²P)CTP to (³²P)CDP-DAG in in vitro reactions that required addition of an exogenous PA substrate. This is a representative histogram comparing the radiolabel incorporated into various cell fractions (membranes, cytosol, and nuclei/unbroken cells) from NCI-H460 cells stably transfected with the hCDS1 cDNA (pCE2.hCDS) or vector only (pCE2). In all fractions, the hCDS1 cDNA increased radiolabel in the organic phase of the reactions. Total CDS activity was much greater in membrane fractions, as would be expected for membrane associated CDS, compared to cytosol fractions. Activity in unbroken cells masked the activity specific to nuclei.

FIG. 6 is a representative phosphorimage of [³²P]phospholipids from membrane fraction CDS assay reactions after the second dimension of ffTLC. FIG. 6 confirms that the radiolabeled product found in the membrane fractions does migrate with a CDP-DAG standard on TLC. The identities of labeled bands were determined by migration of phospholipid standards visualized by UV or FL imaging on the STORM after primulin staining. Lanes 1-3 represent triplicate samples derived from membranes of NCI-H460 cells transfected with the hCDS1 expression vector, and lanes 4-6 represent triplicate samples from transfectants with the control vector. Cells transfected with the hCDS1 cDNA showed 1.6-2.4 fold more CDS activity in membrane fractions than vector transfectants. The relative CDS activity between hCDS1 transfectants and vector transfectants was similar when determined by scintillation counting or TLC analysis. These data indicate that the hCDS1 cDNA clone of SEQ ID NO. 1 does encode CDS activity.

FIGS. 7A and 7B show, respectively, that production of TNF-α (tumor necrosis factor alpha) and IL-6 in ECV304 cells stably transfected with a hCDS1 expression vector increases by greater than five fold relative to ECV304 cells stably transfected with control vector after equal stimulation with IL-1β (interleukin-1 beta). There was little effect on basal level of cytokine release. These data indicate that overexpression of hCDS1 amplified the cytokine signaling response in these cells, as opposed to enhancing steady state, basal signals.

FIG. 8 shows the DNA and amino acid sequence of hCDS2.

FIG. 9 shows an amino acid sequence alignment of the hCDS2 coding sequence with the hCDS1 coding sequence. The amino acids that are identical between the two sequences are highlighted.

FIG. 10 shows the results of a TLS analysis of hCDS2 production of [32P]CDP-DAG after TLC analysis

FIG. 11 shows expression of hCDS1 and hCDS2 mRNAs in cancer versus normal prostate tissues.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides novel, isolated, biologically active mammalian CDS enzymes. The term “isolated” means any CDS polypeptide of the present invention, or any other gene encoding CDS polypeptide, which is essentially free of other polypeptides or genes, respectively, or of other contaminants with which the CDS polypeptide or gene might normally be found in nature.

The invention includes a biologically active polypeptide, CDS, and biologically active fragments thereof. As used herein, the term “biologically active polypeptide” refers to a polypeptide which possesses a biological function or activity which is identified through a biological assay, preferably cell-based, and which results in the formation of CDS-DAG species from PA. A “biologically active polynucleotide” denotes a polynucleotide which encodes a biologically active polypeptide. The term “biologically active fragment,” as used herein, refers to a nucleotide or polypeptide sequence in which one or more amino acids or nucleotides has been deleted but which retains CDS activity.

Minor modification of the CDS primary amino acid sequence may result in proteins which have substantially equivalent activity as compared to the sequenced CDS polypeptide described herein. Such modifications may be deliberate, as by site-directed mutagenesis, or may be spontaneous. All of the polypeptides produced by these modifications are included herein as long as the activity of CDS is present. This can lead to the development of a smaller active molecule which would have broader utility. For example, the present invention includes removal of one or more amino, carboxy terminal, or internal amino acids from the CDS polypeptide, so long as such amino acids are not required for CDS activity.

The CDS polypeptide of the present invention also includes conservative variations of the polypeptide sequence. The term “conservative variation” denotes the replacement of an amino acid residue by another, biologically active similar residue. Examples of conservative variations include the substitution of one hydrophobic residue, such as isoleucine, valine, leucine or methionine for another, or the substitution of one polar residue for another, such as the substitution of arginine for lysine, glutamic for aspartic acids, or glutamine for asparagine, and the like. The term “conservative variation” also includes the use of a substituted amino acid in place of parent amino acid provided that antibodies raised to the substituted polypeptide also immunologically react with the unsubstituted polypeptide.

The present invention further includes allelic variations (naturally-occurring base changes in the species population which may or may not result in an amino acid change) of the DNA sequences herein encoding active CDS polypeptides and active fragments thereof.

The inventive DNA sequences further comprise those sequences which hybridize under high stringency conditions (see, for example, Maniatis et al, Molecular Cloning (A Laboratory Manual), Cold Spring Harbor Laboratory, pages 387-389, 1982) to the coding region of hCDS1 (e.g., nucleotide #150 to nucleotide #1535 in SEQ ID NO. 1) or the coding region of hCDS2 (FIG. 8) and which have CDS activity. High stringency conditions include 5×SSC at 65° C., followed by washing in 0.1×SSC at 65° C. for thirty minutes or, alternatively, 50% formamide, 5×SSC at 42° C.

The present invention also includes nucleotide sequences having at least an 85%, at least a 90%, or at least a 95% sequence identity to the nucleotide sequence of the coding region of hCDS2 (FIG. 8) and which have CDS activity. The present invention further includes a polypeptide having at least an 85%, at least a 90%, or at least a 95% sequence identity to the hCDS2 polypeptide shown in FIG. 8 and which have CDS activity. As used herein, the term “sequence identity” denotes the “match percentage” calculated by the DNASIS computer program (Version 2.5 for Windows; available from Hitachi Software Engineering Co., Ltd., South San Francisco, Calif.) using standard defaults as described in the reference manual accompanying the software, which is incorporated herein by reference.

With regard to the above-described fragments of hCDS2, sequences that hybridize to hCDS2, and sequences having sequence identity to hCDS2, the invention includes embodiments where these sequences have an intact CDS N-terminal region.

The present invention further includes DNA sequences which code for CDS polypeptides having CDS activity but differ in codon sequence due to degeneracy of the genetic code. Variations in the DNA sequences which are caused by point mutations or by induced modifications of the sequence of SEQ ID NO. 1 or FIG. 8, which enhance the activity of the encoded polypeptide or production of the encoded CDS polypeptide are also encompassed by the present invention.

CDS Sequence Discovery

hCDS1

A homology search of the Genbank database (Boguski, et al., Science 265: 1993-1994, 1994) of expressed sequence tags (dbEST) using Drosophila CDS protein sequence as a probe came up with several short stretches of cDNA sequence with homology to the Drosophila CDS protein sequence. These cDNA sequences were derived from single-run partial sequencing of random human cDNA clones carried out mainly by I.M.A.G.E. Consortium [LLNL] cDNA clones program. An example of the amino acid sequence homology between the Drosophila CDS and a human cDNA clone (IMAGE Clone ID #135630) is shown below: 372 KRAFKIKDFGDMIPGHGGIMDRFDCQFLMATFVNVYIS 408 KRAFKIKDF + IPGHGGIMDRFDCQ+LMATFV+VYI+ 11 KRAFKIKDFANTIPGHGGIMDRFDCQYLMATFVHVYIT 124

The top line (SEQ ID NO. 3) refers to the Drosophila CDS sequence from amino acids 371 to 408 and the bottom line (SEQ ID NO. 4) refers to a homologous region from IMAGE Clone ID #135630 translated using reading frame +2. Identical amino acids between these two sequences are shown on the middle line with the “+” signs indicating conservative amino acid changes. In order to determine if such cDNA clones with this level of homology to the Drosophila CDS sequence encoded human CDS sequence, it was necessary to isolate the full-length cDNA clone, insert it into an expression vector, and test if cells transfected with the cDNA expression vector will produce more CDS activity.

Accordingly, a synthetic oligonucleotide (o.h.cds.1R), 5′-CCCACCATGG CCAGGAATGG TATTTGC-3′ (SEQ ID NO. 5), was made based on the complement sequence of the amino acid region, ANTIPGHGG, of IMAGE Clone ID #135630 for the isolation of a putative human cDNA clone from a SuperScript human leukocyte cDNA library (Life Technologies, Gaithersburg, Md.) using the GeneTrapper cDNA positive selection system (Life Technologies, Gaithersburg, Md.). The colonies obtained from positive selection were screened with a [γ-³²P]-ATP labeled synthetic oligonucleotide (o.h.cds.1), 5′-AGTGATGTGA ATTCCTTCGT GACAG-3′ (SEQ ID NO. 6), corresponding to nucleotides 144-168 of IMAGE Clone ID #133825. Of the few cDNA clones that hybridized with the o.h.cds.1 probe, clone LK64 contained the largest cDNA insert with a size of 1700 base pairs. DNA sequence analysis of LK64 showed the translated sequence of its largest open reading frame from the 5′ end contained extensive homology with amino acids 109 to 448 of the Drosophila CDS protein sequence. Clone LK64 did not appear to contain a full-length cDNA insert for CDS. It was missing the coding region corresponding to the first 110 amino acids from the N-terminus. A second homology search of the Genbank database (Boguski, et al., Science 265: 1993-1994, 1994) using the 3′-untranslated sequence of LK64 as a probe came up with more short stretches of cDNA sequences with perfect homology to the 3′ end of the putative human CDS clone LK64. Restriction mapping and DNA sequence analysis of IMAGE Clone ID #145253 (Genome Systems, St. Louis, Mo.), derived from a placental cDNA library, showed it contained extensive sequence homology with the N-terminal coding region of the Drosophila CDS and overlapped with the sequence obtained from clone LK64.

To assemble the putative full-length human CDS cDNA clone, a 500 base pair Pst I-Nco I fragment from of IMAGE Clone ID #145253 and a 1500 base pair Nco I-Not I fragment from LK64 were isolated. These two fragments were inserted into a Pst I and Not I digested vector pBluescriptII SK(−) vector via a three-part ligation to generate pSK.hcds.

FIG. 1 shows the cDNA sequence of hCDS1. The nucleotide sequence analysis and restriction mapping of the cDNA clone revealed a 5′-untranslated region of 1.49 base pairs, an open reading frame encoding a 461 amino acids polypeptide that spans nucleotide positions 150 to 1535 and a 3′-untranslated region of 520 base pairs (FIG. 2). The ATG initiation site for translation was identified at nucleotide positions 150-152 and fulfilled the requirement for an adequate initiation site. (Kozak, Critical Rev. Biochem. Mol. Biol. 27: 385-402, 1992). There was another upstream ATG at positions 4-6 but it was followed by an in-phase stop codon at positions 19-20. The calculated molecular weight of hCDS1 is 53,226 daltons with a predicted pI of 7.57.

The sequence of the 461 amino acid open reading frame (FIG. 3) was used as the query sequence to search for homologous sequences in protein databases. A search of Genbank Release 92 from the National Center for Biotechnology Information (NCBI) using the BLAST program showed that this protein was most homologous to the Drosophila CDS, the yeast CDS, and the E. coli CDS. FIG. 4 shows amino acid sequence alignment of this putative human CDS coding sequence with the Drosophila CDS, the yeast CDS, and the E. coli coding sequences, showing that the human CDS is most homologous to the Drosophila CDS.

hCDS2

A homology search of the Genbank database (Boguski, et al., Science 265: 1993-1994, 1994) of expressed sequence tags (dbEST) using the hCDS1 protein sequence (Weeks et al, DNA Cell Biol. 16: 281-289, 1997) as probe came up with several short stretches of human cDNA sequences that were homologous but distinct from the hCDS1 sequence. These cDNA sequences were derived from single-run partial sequencing of random human cDNA clones projects carried out mainly by I.M.A.G.E. Consortium [LLNL] cDNA clones program.

Of these sequences, IMAGE Clone ID#485825 was found to have the following homology to the coding region of hCDS1 from amino acids 227-271:         10        20        30        40 QSHLVIHNLFEGMIWFIVPISCVICNDIMAYMFGFFFGRTPLIKL X:::::.:::::::::.::::.:::::: ::.::::::::::::: QSHLVIQNLFEGMIWFLVPISSVICNDITAYLFGFFFGRTPLIKL  230       240       250       260       270

The top line refers to IMAGE Clone ID#485825 translated using reading frame+3 and the bottom line refers to the coding region of hCDS1 from amino acids 227-271. Identical amino acids between these two sequences are shown on the middle line as “:” and with the “.” signs indicating conservative amino acid changes. Since the 5′-end of the cDNA insert of IMAGE Clone ID#485825 corresponded to amino acid 227 of hCDS1, this clone therefore does not appear to contain a full-length cDNA insert for CDS, most likely missing the coding region corresponding to the first 220 amino acids from the N-terminus. A second homology search of the Genbank database (Boguski, et al., Science 265: 1993-1994, 1994) of expressed sequence tags (dbEST) using the sequence of IMAGE Clone ID#485825 as probe came up with a clone with a longer cDNA insert (clone ID#663789) from the Genbank database with perfect homology to the IMAGE Clone ID#485825. Restriction mapping and DNA sequence analysis of IMAGE Clone ID#663789 (Genome Systems, St. Louis, Mo.) showed it to be a longer cDNA clone with extensive sequence homology with the coding region of hCDS1 but still missing the first 60 amino acids in the coding region. To isolate the 5′-coding region of hCDS2 cDNA, a synthetic oligonucleotide, 5′-AGGACGCATA TGAGTGGTAG AC-3′ (oCDS2_(—)2R), complementary to a region spanning the Nde I site near the 5′ portion of clone ID#663789 was used in combination with a forward vector primer (o.sport.1), 5′-GACTCTAGCC TAGGCTTTTG C-3′ for amplification of the 5′-region from a pCMV. SPORT human leukocyte cDNA library (Life Technologies, Gaithersburg, Md.). PCR fragments generated that were >400 bp were inserted into the pGEM-T vector (Promega, Madison, Wis.) for further analysis. Restriction mapping and DNA sequence analysis showed one of the clones, pCDS2.H7, to be homologous to the N-terminal coding region of hCDS1.

To assemble the putative full-length human CDS cDNA clone, the 420 bp Acc65 I-Nde I fragment from pCDS2.H7 and the 1200 bp Nde I-Xba I fragment from clone ID#663789 were isolated. These two fragments were inserted into a Acc65 I and Xba I digested vector pBluescript SK(−)II vector via a three-part ligation to generate pSK.CDS2.

FIG. 8 shows the DNA sequence ID of the hCDS2. The nucleotide sequence analysis and restriction mapping of the cDNA clone revealed a 5′-untranslated region of 24 bp, an open reading frame capable of encoding a 445 amino acid polypeptide that spans nucleotide positions 25 to 1362 and a 3′-untranslated region of 1126 bp. The ATG initiation site for translation was localized at nucleotide positions 25-27 and fulfilled the requirement for an adequate initiation site according to Kozak (Kozak, Critical Rev. Biochem. Mol. Biol. 27: 385-402, 1992).

Amino acid sequence alignment of the hCDS2 coding sequence with the human CDS 1 shows 64% identity (FIG. 9). The amino acids that are identical between the two sequences are highlighted.

Expression of Human CDS cDNA in Mammalian Cells

hCDS1

To see if overexpression of hCDS1 would have any effect on mammalian cells, the entire cDNA insert (˜2,000 base pairs) from pSK.hcds was cleaved with Asp718 I and Not I for insertion into the mammalian expression vector pCE2 to generate pCE2.hCDS. The plasmid pCE2 was derived from pREP7b (Leung et al. Proc. Natl. Acad. Sci. USA, 92: 4813-4817, 1995) with the RSV promoter region replaced by the CMV enhancer and the elongation factor-1α (EF-1α) promoter and intron. The CMV enhancer came from a 380 base pair Xba I-Sph I fragment produced by PCR from pCEP4 (Invitrogen, San Diego, Calif.) using the primers 5′-GGCTCTAGAT ATTAATAGTA ATCAATTAC-3′ (SEQ ID NO. 7) and 5′-CCTCACGCAT GCACCATGGT AATAGC-3′ (SEQ ID NO. 8). The EF-1α promoter and intron (Uetsuki et al., J. Biol. Chem., 264: 5791-5798, 1989) came from a 1200 base pair Sph I-Asp718 I fragment produced by PCR from human genomic DNA using the primers 5′-GGTGCATGCG TGAGGCTCCG GTGC-3′ (SEQ ID NO. 9) and 5′-GTAGTTTTCA CGGTACCTGA AATGGAAG-3′ (SEQ ID NO. 10). These 2 fragments were ligated into a Xba I/Asp718 I digested vector derived from pREP7b to generate pCE2.

A second clone, pCE2.hCDS2, was constructed that lacked the human CDS 3′-UT region (520 nt). An Asp718 I (in the multiple cloning site)/NcoI fragment and a NcoI/BamHI fragment from pSK.hCDS were combined in a three-part ligation with Asp718 I/BamHI digested pCE2. Northern blot analysis of 293-EBNA human embryonic kidney cells transiently transfected with CDS cDNA expression plasmids (pCE2.hCDS or pCE2.hCDS2) showed that deletion of the entire 3′-UT region had little effect on CDS steady-state mRNA levels.

The CDS activity in transfected cell fractions (membranes, cytosol, nuclei/unbroken cells) was determined by incorporation of (α-³²P)CTP into (³²P)CDP-DAG in the presence of exogenously added PA substrate. Cells were fractionated by resuspending previously frozen cell pellets in cold hypotonic lysis buffer (HLB; 10 mM KCl, 1.5 mM MgCl₂, 10 mM Tris, pH 7.4, 2 mM benzamidine HCl, and 10 μg/ml each leupeptin, soybean trypsin inhibitor, and pepstatin A) at approx. 5×10⁷ cells/ml. After 10 min. on ice, cells were dounced (Wheaton pestle A) 40 strokes, then spun 500×g, 10 min. at 4° C. to remove nuclei and unbroken cells. The resuspension of the pellet, incubation, and low speed spin were repeated twice. The final “nuclei/unbroken cells” pellet was resuspended in 50-100 μl HLB. Supernatants were spun at 109,000×g, 30 min. at 4° C. generating “cytosol” supernates and “membrane” pellets. The pellets were resuspended in 150-225 μl HLB. An aliquot of each fraction was removed for determination of protein concentration by a BCA assay. Fractions were stored at −70° C. All assays were done on fractions after one thaw.

The in vitro CDS activity assay conditions were a modification of methods described previously (Mok et al., FEBS Letters 312: 236-240, 1992; and Wu et al., Nature 373: 216-222, 1995). Briefly, each 0.3 ml reaction combined 0.23 mM PA (Sigma; from egg yolk lecithin), 50 mM Tris-maleate, pH 7.0, 1.5% Triton X-100, 0.5 mM DTT, 75-500 μg protein from cell fractions, 30 mM MgCl₂, and 2 μCi (α-³²P)CTP. MgCl₂ and (α-³²P)CTP were added just prior to a 10 min. incubation at 37° C. The reactions were terminated with 4 ml chloroform:methanol (1:1) and vortexing. The organic phase was extracted three times with 1.8 ml 0.1N HCl with 1 M NaCl, and vortexing. Radioactivity in the organic phase was determined by scintillation counting or TLC.

A flip-flop TLC (ffTLC) system (Gruchalla et al., J. Immunol. 144: 2334-2342, 1990) was modified for the separation of CDP-DAG and PA. Specifically, 200 ml of organic phase was dried and brought up in 20 μL CHCl₃:MeOH (2:1) and spotted in the center of a 20×20 cm TLC plate (Analtech Silica Gel HP-HLF). TLC was run in CHCl₃:MeOH:NH₄OH:H₂O (65:30:4:1) until the solvent had reached the top of the plate. In this solvent system, neutral and cationic lipids migrate, whereas PA, CDP-DAG and other anionic lipids stay near the origin. The plate was dried and visualized by UV with 0.05% primulin stain (Sigma, St. Louis, Mo.) in 80% acetone. The plate was cut below the PC standard, and the bottom half of the plate was rotated 180° and run in CHCl₃:MeOH:Acetic Acid:H₂O (80:25:15:5) to enable migration of the anionic lipids until the solvent reached the top of the plate. The radioactive bands on the TLC plate were quantified using a. STORMS phosphorimager (Molecular Dynamics, Sunnyvale, Calif.). Non-radiolabeled lipid standards were stained with primulin and visualized by fluorescence using the STORM®.

FIG. 5 shows the results of in vitro CDS activity assays on cell fractions from stable transfectants of NCI-H460 cells. CDS activity was assessed by conversion of (α-³²P)CTP to (³²P)CDP-DAG in in vitro reactions that required addition of an exogenous PA substrate. This is a representative histogram comparing the radiolabel incorporated into various cell fractions (membranes, cytosol, and nuclei/unbroken cells) from NCI-H460 cells stably transfected with the hCDS1 cDNA (pCE2.hCDS) or vector only (pCE2). In all fractions, the CDS cDNA increased radiolabel in the organic phase of the reactions. Total CDS activity was much greater in membrane fractions, as would be expected for membrane associated CDS, compared to cytosol fractions. Activity in unbroken cells masked the activity specific to nuclei.

FIG. 6 is a representative phosphorimage of [³²P]phospholipids from membrane fraction CDS assay reactions after the second dimension of ffTLC. FIG. 6 confirms that the radiolabeled product found in the membrane fractions does migrate with a CDP-DAG standard on TLC. The identities of labeled bands were determined by migration of phospholipid standards visualized by UV or FL imaging on the STORM after primulin staining. Lanes 1-3 represent triplicate samples derived from membranes of NCI-H460 cells transfected with the hCDS1 expression vector, and lanes 4-6 represent triplicate samples from transfectants with the control vector. Cells transfected with the hCDS1 cDNA showed 1.6-2.4 fold more CDS activity in membrane fractions than vector transfectants. The relative CDS activity between CDS transfectants and vector transfectants was similar when determined by scintillation counting or TLC analysis. Similar CDS activity was seen in two different transfected human cell lines, NCI-H460 and ECV304. The average specific activity of CDS in membranes of CDS transfectants was 2.7 fmol/min/mg protein compared to 1.4 fmol/min/mg protein in membranes of vector transfectants. These results demonstrated that overexpression of the human CDS cDNA clone lead to an increase in CDS activity in cell fractions and that activity in an in vitro assay was completely dependent on the addition of PA. These data indicate that the human cDNA clone of SEQ ID NO. 1 does encode CDS activity.

hCDS2

To see if overexpression of hCDS2 has an effect in mammalian cells, the entire cDNA insert (˜1,900 bp) from pSK.CDS2 was cleaved with Asp718 I and Xba I for insertion into a mammalian inducible expression vector pIND (Invitrogen, San Diego, Calif.) to generate pI_CDS2.

pI_CDS2 DNA and pVgRXR (Invitrogen, San Diego, Calif.) DNA were co-transfected into ECV304 cells (American Type Culture Collection, Rockville, Md.) with a Cell-Porator™ (Life Technologies, Gaithersburg, Md.) using conditions described previously (Cachianes, et al., Biotechniques 15: 255-259, 1993). After adherence of the transfected cells 24 hours later, the cells were grown in the presence of 500 μg/ml G418 (Life Technologies, Gaithersburg, Md.) and 100 μg/ml Zeocin (Invitrogen, San Diego, Calif.) to select for cells that had incorporated both plasmids. G418 and Zeocin resistant clones that expressed CDS2 mRNA at a level more than 10 fold higher in the presence of muristerone A (Invitrogen, San Diego, Calif.) relative to uninduced or untranfected cells based on Northern Blot analysis (Kroczek, et al., Anal. Biochem. 184: 90-95, 1990) were selected for further study.

The CDS activity in ECV304 cells transfected with pI_CDS2 DNA and pVgRXR DNA with or without muristerone A induction was compared using a TLC assay (Weeks et al, DNA Cell Biol. 16: 281-289, 1997).

FIG. 10 shows an example of hCDS2 assay results by measuring the production of [32P]CDP-DAG after TLC analysis. The identities of labeled bands were determined based on Rf values obtained for standard phospholipids visualized by primulin staining. The left two bars represent triplicate samples derived from ECV304 cells transfected with pVgRXR and the control vector pIND in the absence or presence of the inducer muristerone A. The enzyme activity found here represents endogenous CDS activity found in ECV304 cells, as cells without or with muristerone A treatment produced similar activity. The right two bars represent triplicate samples derived from ECV304 cells transfected with pVgRXR and the inducible CDS2 vector pI_CDS2 in the absence or presence of the inducer muristerone A. Quantitation of the radioactive bands corresponding to CDP-DAG shows cells transfected with the inducible hCDS2 expression plasmid have an approximately two fold increase in activity after induction with muristerone A compared to same cells without induction or to vector control cells either with or without induction, showing that the hCDS2 cDNA clone encode a protein having CDS activity.

Complementation of Yeast cds1 Mutant with hCDS1

As the yeast CDS gene is essential for growth (Shen et al., J. Biol. Chem. 271: 789-795, 1996), another way to show that the cDNA does encode CDS activity was to determine if the human CDS cDNA will complement the growth defect of a mutant yeast strain with a deletion in the endogenous yeast CDS gene. Accordingly, the hCDS1 cDNA was cloned downstream of a GAL1 promoter in a yeast expression vector. Specifically, a Hind III-Sac I fragment from pSK.hCDS was inserted into pYES.LEU vector to generate pYES.hCDS. pYES.LEU was derived from pYES2 (Invitrogen, San Diego, Calif.) by inserting a BspH I fragment containing a LEU2 marker from pRS315 (Sikorski et al., Genetics 122: 19-27, 1989) into the Nco I of pYES2. pYES.hCDS was introduced into a null cds1 strain of yeast, YSD90A (Shen et al., J. Biol. Chem. 271: 789-795, 1996), with a covering plasmid, pSDG1, carrying the functional yeast CDS1. The latter plasmid was cured from cells by growth in media lacking leucine but containing uracil and galactose. PCR analysis confirmed the absence of the yeast CDS1 gene and Northern blot analysis verified expression of the hCDS1 cDNA. This strain was found to be absolutely dependent on galactose for growth. Galactose activates the GAL1 promoter for the production of human CDS protein. When the carbon source was switched to glucose, which would shut down the GAL1 promoter, growth stopped completely in less than a generation. These data show the human CDS was able to complement the growth defect of a yeast cds1 mutant.

The cells grown on galactose were lysed and assayed for CDS activity according to the assay method described (Shen et al., J. Biol. Chem. 271: 789-795, 1996). The specific activity using yeast conditions showed activity at 20% of single copy CDS1 wild type activity. This is consistent with the above plasmid in a wild type background showing approximately 1.3 fold increase in activity when grown on galactose versus glucose.

The following experiment found that hCDS1 over-expression enhanced cytokine induced signaling in cells. Over-expression of CDS was expected to alter the cellular level of various lipid second messengers such as PA, IP₃ and DAG (Kent, Anal. Rev. Biochem. 64: 315-343, 1995) and hence modulates cytokine induced signaling response in cells. To test this hypothesis, a hCDS1 expression plasmid (pCE2.hCDS), or vector (pCE2) were stably transfected into ECV304 cells (American Type Culture Collection, Rockville, Md.), an endothelial cell line that produces IL-6 and TNF-α upon stimulation with IL-1β. FIG. 7 shows that the secretion of TNF-α IL-6 in ECV304 cells stably transfected with CDS expression vector increased by >5 fold relative to ECV304 cells stably transfected with control vector after stimulation with 1 ng/ml IL-1β. However, there was little effect on the basal level of cytokine release, suggesting that over-expression of CDS amplified the cytokine signaling response, as opposed to enhancing the steady-state, basal signal, in these cells.

Expression of hCDS1 and hCDS2 mRNA in Cancer Versus Normal Prostate Tissue

To examine if CDS mRNA expression in cancer versus normal tissues, RT-PCR was performed on specimens of prostate cancer tissues and the corresponding normal prostate tissues in the surgical margins from four independent patients. FIG. 11 shows hCDS1 mRNA was elevated in prostate cancer in 2 out of 4 patients, whereas hCDS2 mRNA was elevated in prostate cancer in 3 out of 4 patients. A housekeeping gene β2-microglobulin mRNA level was found to be similar in normal and cancer prostate tissues. ETS-2, a transcription factor reported to be elevated in prostate cancer (Liu et al., Prostate 30: 145-153, 1997), was found to be elevated in the same 3 out of 4 patients examined here, suggesting hCDS2, like ETS-2, may be a target for drug intervention in cancer therapy.

CDS Polypeptide Synthesis

Polypeptides of the present invention can be synthesized by such commonly used methods as t-BOC or FMOC protection of alpha-amino groups. Both methods involve step-wise syntheses whereby a single amino acid is added at each step starting from the C-terminus of the peptide (Coligan et al., Current Protocols in Immunology, Wiley Interscience, Unit 9, 1991). In addition, polypeptides of the present invention can also be synthesized by solid phase synthesis methods (e.g., Merrifield, J. Am. Chem. Soc. 85: 2149, 1962; and Steward and Young, Solid Phase Peptide Synthesis, Freeman, San Francisco pp. 27-62, 1969) using copolyol (styrene-divinylbenzene) containing 0.1-1.0 mM amines/g polymer. On completion of chemical synthesis, the polypeptides can be deprotected and cleaved from the polymer by treatment with liquid HF 10% anisole for about 15-60 min at 0° C. After evaporation of the reagents, the peptides are extracted from the polymer with 1% acetic acid solution, which is then lyophilized to yield crude material. This can normally be purified by such techniques as gel filtration of Sephadex G-15 using 5% acetic acid as a solvent. Lyophilization of appropriate fractions of the column will yield a homogeneous polypeptide or polypeptide derivatives, which are characterized by such standard techniques as amino acid analysis, thin layer chromatography, high performance liquid chromatography, ultraviolet absorption spectroscopsy, molar rotation, solubility and quantitated by solid phase Edman degradation.

CDS Polynucleotides

The invention also provides polynucleotides which encode the CDS polypeptide of the invention. As used herein, “polynucleotide” refers to a polymer of deoxyribonucleotides or ribonucleotides in the form of a separate fragment or as a component of a larger construct. DNA encoding the polypeptide of the invention can be assembled from cDNA fragments or from oligonucleotides which provide a synthetic gene which is capable of being expressed in a recombinant transcriptional unit. Polynucleotide sequences of the invention include DNA, RNA and cDNA sequences. Preferably, the nucleotide sequence encoding CDS is the sequence of SEQ ID NO. 1 or of FIG. 8. DNA sequences of the present invention can be obtained by several methods. For example, the DNA can be isolated using hybridization procedures which are known in the art. Such hybridization procedures include, for example, hybridization of probes to genomic or cDNA libraries to detect shared nucleotide sequences, antibody screening of expression libraries to detect common antigenic epitopes or shared structural features and synthesis by the polymerase chain reaction (PCR). Such hybridization includes hybridization under high stringency conditions as described above.

Hybridization procedures are useful for screening recombinant clones by using labeled mixed synthetic oligonucleotides probes, wherein each probe is potentially the complete complement of a specific DNA sequence in a hybridization sample which includes a heterogeneous mixture of denatured double-stranded DNA. For such screening, hybridization is preferably performed on either single-stranded DNA or denatured double-stranded DNA. Hybridization is particularly useful for detection of cDNA clones derived from sources where an extremely low amount of mRNA sequences relating to the polypeptide of interest are present. Using stringent hybridization conditions to avoid non-specific binding, it is possible to allow an autoradiographic visualization of a specific genomic DNA or cDNA clone by the hybridization of the target DNA to a radiolabeled probe, which is its complement (Wallace et al. Nucl. Acid Res. 9: 879, 1981). Specific DNA sequences encoding CDS can also be obtained by isolation and cloning of double-stranded DNA sequences from the genomic DNA, chemical manufacture of a DNA sequence to provide the necessary codons for the complete polypeptide of interest or portions of the sequence for use in PCR to obtain the complete sequence, and in vitro synthesis of a double-stranded DNA sequence by reverse transcription of mRNA isolated from a eukaryotic donor cell. In the latter case, a double-stranded DNA complement of mRNA is eventually formed which is generally referred to as cDNA. Of these three methods for developing specific DNA sequences for use in recombinant procedures, the isolation of cDNA clones is the most useful. This is especially true when it is desirable to obtain the microbial expression of mammalian polypeptides since the presence of introns in genomic DNA clones can prevent accurate expression.

The synthesis of DNA sequences is sometimes a method that is preferred when the entire sequence of amino acids residues of the desired polypeptide product is known. When the entire sequence of amino acid residues of the desired polypeptide is not known, direct synthesis of DNA sequences is not possible and it is desirable to synthesize cDNA sequences. cDNA sequence isolation can be done, for example, by formation of plasmid- or phage-carrying cDNA libraries which are derived from reverse transcription of mRNA. mRNA is abundant in donor cells that have high levels of genetic expression. In the event of lower levels of expression, PCR techniques can be used to isolate and amplify the cDNA sequence of interest. Using synthesized oligonucleotides corresponding exactly, or with some degeneracy, to known CDS amino acid or nucleotide sequences, one can use PCR to obtain and clone the sequence between the oligonucleotides. The oligonucleotide may represent invariant regions of the CDS sequence and PCR may identify sequences (isoforms) with variations from SEQ ID NO. 1 or FIG. 8.

A cDNA expression library, such as lambda gt11, can be screened indirectly for the CDS polypeptide, using antibodies specific for CDS. Such antibodies can be either polyclonal or monoclonal, derived from the entire CDS protein or fragments thereof, and used to detect and isolate expressed proteins indicative of the presence of CDS cDNA.

A polynucleotide sequence can be deduced from an amino acid sequence by using the genetic code, however the degeneracy of the code must be taken into account. Polynucleotides of this invention include variant polynucleotide sequences which code for the same amino acids as a result of degeneracy in the genetic code. There are 20 natural amino acids, most of which are specified by more that one codon (a three base sequence). Therefore, as long as the amino acid sequence of CDS results in a biologically active polypeptide (at least, in the case of the sense polynucleotide strand), all degenerate nucleotide sequences are included in the invention. The polynucleotide sequence for CDS also includes sequences complementary to the polynucleotides encoding CDS (antisense sequences). Antisense nucleic acids are DNA, and RNA molecules that are complementary to at least a portion of a specific mRNA molecule (Weintraub, Sci. Amer. 262: 40, 1990). The invention embraces all antisense polynucleotides capable of inhibiting the production of CDS polypeptide. In the cell, the antisense nucleic acids hybridize to the corresponding mRNA, forming a double-stranded molecule. The antisense nucleic acids interfere with the translation of mRNA since the cell cannot translate mRNA that is double-stranded. Antisense oligomers of about 15 nucleotides are preferred, since they are easily synthesized and are less likely to cause problems than larger molecules when introduced into the target CDS-producing cell. The use of antisense methods to inhibit translation of genes is known (e.g., Marcus-Sakura, Anal. Biochem. 172: 289, 1988).

In addition, ribozyme nucleotide sequences for CDS are included in this invention. Ribozymes are hybrid RNA:DNA molecules possessing an ability to specifically cleave other single-stranded RNA in a manner analogous to DNA restriction endonucleases. Through the modification of nucleotide sequences which encode such RNAs, it is possible to engineer molecules that recognize specific nucleotide sequences in an RNA molecule and cleave it (Cech, J. Amer. Med. Assn. 260: 3030, 1988). An advantage of this approach is that only mRNAs with particular sequences are inactivated because they are sequence-specific.

The CDS DNA sequence may be inserted into an appropriate recombinant expression vector. The term “recombinant expression vector” refers to a plasmid, virus or other vehicle that has been manipulated by insertion or incorporation of the genetic sequences. Such expression vectors contain a promoter sequence which facilitates efficient transcription of the inserted genetic sequence in the host. The expression vector typically contains an origin of replication, a promoter, as well as specific genes which allow phenotypic selection of the transformed cells. Vectors suitable for use in the present invention include, for example, vectors with a bacterial promoter and ribosome binding site for expression in bacteria (Gold, Meth. Enzymol. 185: 11, 1990), expression vectors with mammalian or viral promoter and enhancer for expression in mammalian cells (Kaufman, Meth. Enzymol. 185: 487, 1990) and baculovirus-derived vectors for expression in insect cells (Luckow et al., J. Virol. 67: 4566, 1993). The DNA segment can be present in the vector operably linked to regulatory elements, for example, constitutive or inducible promoters (e.g., T7, metallothionein I, CMV, or polyhedren promoters).

The vector may include a phenotypically selectable marker to identify host cells which contain the expression vector. Examples of markers typically used in prokaryotic expression vectors include antibiotic resistance genes for ampicillin (β-lactamases), tetracycline and chloramphenicol (chloramphenicol acetyltransferase). Examples of such markers typically used in mammalian expression vectors include the gene for adeno sine deaminase (ADA), aminoglyco side phosphotransferase (neo, G418), dihydrofolate reductase (DHFR), hygromycin-B-phosphotransferase (HPH), thymidine kinase (TK), and xanthine guanine phosphoriboseyltransferase (XGPRT, gpt).

In another preferred embodiment, the expression system used is one driven by the baculovirus polyhedrin promoter. The gene encoding the polypeptide can be manipulated by standard techniques in order to facilitate cloning into the baculovirus vector. A preferred baculovirus vector is the pBlueBac vector (Invitrogen, Sorrento, Calif.). The vector carrying the gene for the polypeptide is transfected into Spodoptera frugiperda (Sf9) cells by standard protocols, and the cells are cultured and processed to produce the recombinant polypeptide. See Summers et al., A Manual for Methods of Baculovirus Vectors and Insect Cell Culture Procedures, Texas Agricultural Experimental Station.

Once the entire coding sequence of the gene for the polypeptides has been determined, the gene can be expressed in any number of different recombinant DNA expression systems to generate large amounts of polypeptide. Included within the present invention are polypeptides having native glycosylation sequences, and deglycosylated or unglycosylated polypeptides prepared by the methods described below. Examples of expression systems known to the skilled practitioner in the art include bacteria such as E. coli, yeast such as Pichia pastoris, baculovirus, and mammalian expression systems such as in COS or CHO cells.

The gene or gene fragment encoding the desired polypeptide can be inserted into an expression vector by standard subcloning techniques. In a preferred embodiment, an E. coli expression vector is used which produces the recombinant protein as a fusion protein, allowing rapid affinity purification of the protein. Examples of such fusion protein expression systems are the glutathione S-transferase system (Pharmacia, Piscataway, N.J.), the maltose binding protein system (NEB, Beverley, Mass.), the thiofusion system (Invotrogen, San Diego, Calif.), the FLAG system (IBI, New Haven, Conn.), and the 6×His system (Qiagen, Chatsworth, Calif.). Some of these systems produce recombinant polypeptides bearing only a small number of additional amino acids, which are unlikely to affect the CDS activity of the recombinant polypeptide. For example, both the FLAG system and the 6×His system add only short sequences, both of which are known to be poorly antigenic and which do not adversely affect folding of the polypeptide to its native conformation. Other fusion systems produce proteins where it is desirable to excise the fusion partner from the desired protein. In a preferred embodiment the fusion partner is linked to the recombinant polypeptide by a peptide sequence containing a specific recognition sequence for a protease. Examples of suitable sequences are those recognized by the Tobacco Etch Virus protease (Life Technologies, Gaithersburg, Md.) or Factor Xa (New England Biolabs, Beverley, Mass.) or enterokinase (Invotrogen, San Diego, Calif.).

Production of Polypeptides

Polynucleotide sequences encoding CDS polypeptides of the invention can be expressed in either prokaryotes or eukaryotes. Hosts can include microbial (bacterial), yeast, insect and mammalian organisms. Methods of expressing DNA sequences inserted downstream of prokaryotic or viral regulatory sequences in prokaryotes are known in the art (Makrides, Microbio. Rev. 60: 512, 1996). Biologically functional viral and plasmid DNA vectors capable of expression and replication in a eukaryotic host are known in the art (Cachianes, Biotechniques 15: 255, 1993). Such vectors are used to incorporate DNA sequences of the invention. DNA sequences encoding the inventive polypeptides can be expressed in vitro by DNA transfer into a suitable host using known methods of transfection.

Sequences encoding CDS polypeptides may be inserted into a recombinant expression vector. The term “recombinant expression vector” refers to a plasmid, virus or other vehicle that has been manipulated by inserting or incorporating genetic sequences. Such expression vectors contain a promoter sequence which facilitates efficient transcription of the inserted genetic sequence of the host. The expression vector typically contains an origin of replication and a promoter, as well as specific genes which allow phenotypic selection of the transformed cells. The DNA segment can be present in the vector, operably linked to regulatory elements, for example, a promoter (e.g., T7, metallothionein I, or polyhedren promoters). Vectors suitable for use in the present invention include, for example, bacterial expression vectors, with bacterial promoter and ribosome binding sites, for expression in bacteria (Gold, Meth. Enzymol. 185: 11, 1990), expression vector with animal promoter and enhancer for expression in mammalian cells (Kaufman, Meth. Enzymol. 185: 487, 1990) and baculovirus-derived vectors for expression in insect cells (Luckow et al., J. Virol. 67: 4566, 1993).

The vector may include a phenotypically selectable marker to identify host cells which contain the expression vector. Examples of markers typically used in prokaryotic expression vectors include antibiotic resistance genes for ampicillin (β-lactamases), tetracycline and chloramphenicol (chloramphenicol acetyltransferase). Examples of such markers typically used in mammalian expression vectors include the gene for adenosine deaminase (ADA), aminoglycoside phosphotransferase (neo, G418), dihydrofolate reductase (DHFR), hygromycin-B-phosphotransferase (HPH), thymidine kinase (TK), and xanthine guanine phosphoriboseyltransferase (XGPRT, gpt).

In another preferred embodiment, the expression system used is one driven by the baculovirus polyhedrin promoter. The polynucleotide encoding CDS can be manipulated by standard techniques in order to facilitate cloning into the baculovirus vector. See Ausubel et al., supra. A preferred baculovirus vector is the pBlueBac vector (Invitrogen, Sorrento, Calif.). The vector carrying a polynucleotide encoding CDS is transfected into Spodoptera frugiperda (Sf9) cells by standard protocols, and the cells are cultured and processed to produce the recombinant polypeptide. See Summers et al., A Manual for Methods of Baculovirus Vectors and Insect Cell Culture Procedures, Texas Agricultural Experimental Station.

The polynucleotides of the present invention can be expressed in any number of different recombinant DNA expression systems to generate large amounts of polypeptide. Included within the present invention are CDS polypeptides having native glycosylation sequences, and deglycosylated or unglycosylated polypeptides prepared by the methods described below. Examples of expression systems known to the skilled practitioner in the art include bacteria such as E. coli, yeast such as Pichia pastoris, baculovirus, and mammalian expression systems such as in Cos or CHO cells.

The polynucleotides of the present invention can be inserted into an expression vector by standard subcloning techniques. In a preferred embodiment, an E. coli expression vector is used which produces the recombinant protein as a fusion protein, allowing rapid affinity purification of the protein. Examples of such fusion protein expression systems are the glutathione S-transferase system (Pharmacia, Piscataway, N.J.), the maltose binding protein system (NEB, Beverley, Mass.), the thiofusion system (Invitrogen, San Diego, Calif.), the Strep-tag II system (Genosys, Woodlands, Tex.), the FLAG system (IBI, New Haven, Conn.), and the 6×His system (Qiagen, Chatsworth, Calif.). Some of these systems produce recombinant polypeptides bearing only a small number of additional amino acids, which are unlikely to affect the CDS ability of the recombinant polypeptide. For example, both the FLAG system and the 6×His system add only short sequences, both of which are known to be poorly antigenic and which do not adversely affect folding of the polypeptide to its native conformation. Other fusion systems produce proteins where it is desirable to excise the fusion partner from the desired protein. In a preferred embodiment, the fusion partner is linked to the recombinant polypeptide by a peptide sequence containing a specific recognition sequence for a protease. Examples of suitable sequences are those recognized by the Tobacco Etch Virus protease (Life Technologies, Gaithersburg, Md.) or Factor Xa (New England Biolabs, Beverley, Mass.) or enterokinase (Invitrogen, San Diego, Calif.).

In an embodiment of the present invention, the polynucleotides encoding CDS are analyzed to detect putative transmembrane sequences. Such sequences are typically very hydrophobic and are readily detected by the use of standard sequence analysis software, such as MacDNASIS (Hitachi, San Bruno, Calif.). The presence of transmembrane sequences is often deleterious when a recombinant protein is synthesized in many expression systems, especially in E coli, as it leads to the production of insoluble aggregates which are difficult to renature into the native conformation of the polypeptide.

Accordingly, deletion of one or more of the transmembrane sequences may be desirable. Deletion of transmembrane sequences typically does not significantly alter the conformation or activity of the remaining polypeptide structure. However, one can determine whether deletion of one or more of the transmembrane sequences has effected the biological activity of the CDS protein by, for example, assaying the activity of the CDS protein containing one or more deleted sequences and comparing this activity to that of unmodified CDS. Examples of assays for CDS activity are described above.

Moreover, transmembrane sequences, being by definition embedded within a membrane, are inaccessible as antigenic determinants to a host immune system. Antibodies to these sequences will not, therefore, provide immunity to the host and, hence, little is lost in terms of generating monoclonal or polyclonal antibodies by omitting such sequences from the recombinant polypeptides of the invention. Deletion of transmembrane-encoding sequences from the polynucleotide used for expression can be achieved by standard techniques. See Ausubel et al., supra, Chapter 8. For example, fortuitously-placed restriction enzyme sites can be used to excise the desired gene fragment, or the PCR can be used to amplify only the desired part of the gene.

Transformation of a host cell with recombinant DNA may be carried out by conventional techniques. When the host is prokaryotic, such as E. coli, competent cells which are capable of DNA uptake can be prepared from cells harvested after exponential growth phases and subsequently treated by a CaCl₂ method using standard procedures. Alternatively, MgCl₂ or RbCl can be used. Transformation can also be performed after forming a protoplast of the host cell or by electroporation.

When the host is a eukaryote, methods of transfection of DNA, such as calcium phosphate co-precipitates, conventional mechanical procedures, (e.g., microinjection), electroporation, liposome-encased plasmids, or virus vectors may be used. Eukaryotic cells can also be cotransformed with DNA sequences encoding CDS polypeptides of the present invention, and a second foreign DNA molecule encoding a selectable phenotype, such as the herpes simplex thymidine kinase gene. Another method uses a eukaryotic viral vector, such as simian virus 40 (SV40) or bovine papilloma virus to transiently infect or transform eukaryotic cells and express the CDS polypeptides.

Expression vectors that are suitable for production of CDS polypeptides preferably contain (1) prokaryotic DNA elements coding for a bacterial replication origin and an antibiotic resistance marker to provide for the growth and selection of the expression vector in a bacterial host; (2) eukaryotic DNA elements that control initiation of transcription, such as a promoter; and (3) DNA elements that control the processing of transcripts, such as a transcription termination/polyadenylation sequence. CDS polypeptides of the present invention preferably are expressed in eukaryotic cells, such as mammalian, insect and yeast cells. Mammalian cells are especially preferred eukaryotic hosts because mammalian cells provide suitable post-translational modifications such as glycosylation. Examples of mammalian host cells include Chinese hamster ovary cells (CHO-K; ATCC CCL61), rat pituitary cells (GH₁; ATCC CCL82), HeLa S3 cells (ATCC CCL2.2), rat hepatoma cells (H-4-II-E; ATCC CRL1548) SV40-transformed monkey kidney cells (COS-1; ATCC CRL 1650) and murine embryonic cells (NIH-3T3; ATCC CRL 1658). For a mammalian host, the transcriptional and translational regulatory signals may be derived from viral sources, such as adenovirus, bovine papilloma virus, simian virus, or the like, in which the regulatory signals are associated with a particular gene which has a high level of expression. Suitable transcriptional and translational regulatory sequences also can be obtained from mammalian genes, such as actin, collagen, myosin, and metallothionein genes.

Transcriptional regulatory sequences include a promoter region sufficient to direct the initiation of RNA synthesis. Suitable eukaryotic promoters include the promoter of the mouse metallothionein I gene (Hamer et al., J. Molec. Appl. Genet. 1: 273, 1982); the TK promoter of Herpes virus (McKnight, Cell 31: 355, 1982); the SV40 early promoter (Benoist et al., Nature 290: 304, 1981); the Rous sarcoma virus promoter (Gorman et al., Proc. Nat'l. Ac Sci. USA 79: 6777, 1982); and the cytomegalovirus promoter (Foecking et al., Gene 45: 101, 1980). Alternatively, a prokaryotic promoter, such as the bacteriophage T3 RNA polymerase promoter, can be used to control fusion gene expression if the prokaryotic promoter is regulated by a eukaryotic promoter (Zhou et al., Mol. Cell. Biol. 10: 4529, 1990; Kaufman et al, Nucl. Acids Res. 19: 4485, 1991).

An expression vector can be introduced into host cells using a variety of techniques including calcium phosphate transfection, liposome-mediated transfection, electroporation, and the like. Preferably, transfected cells are selected and propagated wherein the expression vector is stably integrated in the host cell genome to produce stable transformants. Techniques for introducing vectors into eukaryotic cells and techniques for selecting stable transformants using a dominant selectable marker are described, for example, by Ausubel and by Murray (ed.), Gene Transfer and Expression Protocols (Humana Press 1991). Examples of mammalian host cells include COS, BHK, 293 and CHO cells.

Purification of Recombinant Polypeptides.

The polypeptide expressed in recombinant DNA expression systems can be obtained in large amounts and tested for biological activity. The recombinant bacterial cells, for example E. coli, are grown in any of a number of suitable media, for example LB, and the expression of the recombinant polypeptide induced by adding IPTG to the media or switching incubation to a higher temperature. After culturing the bacteria for a further period of between 2 and 24 hours, the cells are collected by centrifugation and washed to remove residual media. The bacterial cells are then lysed, for example, by disruption in a cell homogenizer and centrifuged to separate the dense inclusion bodies and cell membranes from the soluble cell components. This centrifugation can be performed under conditions whereby the dense inclusion bodies are selectively enriched by incorporation of sugars such as sucrose into the buffer and centrifugation at a selective speed. If the recombinant polypeptide is expressed in the inclusion, these can be washed in any of several solutions to remove some of the contaminating host proteins, then solubilized in solutions containing high concentrations of urea (e.g., 8 M) or chaotropic agents such as guanidine hydrochloride in the presence of reducing agents such as β-mercaptoethanol or DTT (dithiothreitol). At this stage it may be advantageous to incubate the polypeptide for several hours under conditions suitable for the polypeptide to undergo a refolding process into a conformation which more closely resembles that of the native polypeptide. Such conditions generally include low polypeptide (concentrations less than 500 mg/ml), low levels of reducing agent, concentrations of urea less than 2 M and often the presence of reagents such as a mixture of reduced and oxidized glutathione which facilitate the interchange of disulphide bonds within the protein molecule. The refolding process can be monitored, for example, by SDS-PAGE or with antibodies which are specific for the native molecule. Following refolding, the polypeptide can then be purified further and separated from the refolding mixture by chromatography on any of several supports including ion exchange resins, gel permeation resins or on a variety of affinity columns.

Isolation and purification of host cell expressed polypeptide, or fragments thereof may be carried out by conventional means including, but not limited to, preparative chromatography and immunological separations involving monoclonal or polyclonal antibodies.

These polypeptides may be produced in a variety of ways, including via recombinant DNA techniques, to enable large scale production of pure, active CDS useful for screening compounds for trilineage hematopoietic and anti-inflammatory therapeutic applications, and developing antibodies for therapeutic, diagnostic and research use.

Screening Assays Using CDS Polypeptides

The CDS polypeptide of the present invention is useful in a screening methodology for identifying compounds or compositions which affect cellular signaling of an inflammatory response. This method comprises incubating the CDS polypeptides or a cell transfected with cDNA encoding CDS, with a suitable substrate, for example, PA, under conditions sufficient to allow the components to interact, and then measuring the effect of the compound or composition on CDS activity. See, for example, above, and Weeks et al., DNA Cell Biol. 16: ₂₈₁-289, 1997. The observed effect on CDS may be either inhibitory or stimulatory. Such compounds or compositions to be tested can be selected from a combinatorial chemical library or any other suitable source (Hogan, Jr., Nat. Biotechnology 15: 328, 1997).

Peptide Sequencing of Polypeptides

Substitutional variants typically contain the exchange of one amino acid for another at one or more sites within the protein, and are designed to modulate one or more properties of the polypeptides such as stability against proteolytic cleavage. Substitutions preferably are conservative, that is, one amino acid is replaced with one of similar shape and charge. Conservative substitutions are well known in the art and include, for example, the changes of alanine to serine; arginine to lysine; asparigine to glutamine or histidine; aspartate to glutamate; cysteine to serine; glutamine to asparigine; glutamate to aspartate; glycine to proline; histidine to asparigine or glutamine; isoleucine to leucine or valine; leucine to valine or isoleucine, lysine to arginine, glutamine, or glutamate, methionine to leucine or isoleucine; phenylalanine to tyrosine, leucine or methionine; serine to threonine; threonine to serine; tryptophan to tyrosine; tyrosine to tryptophan or phenylalanine; and valine to isoleucine or leucine. Insertional variants contain fusion proteins such as those used to allow rapid purification of the polypeptide and also can include hybrid polypeptides containing sequences from other proteins and polypeptides which are homologues of the inventive polypeptide. For example, an insertional variant could include portions of the amino acid sequence of the polypeptide from one species, together with portions of the homologous polypeptide from another species. Other insertional variants can include those in which additional amino acids are introduced within the coding sequence of the polypeptides. These typically are smaller insertions than the fusion proteins described above and are introduced, for example, to disrupt a protease cleavage site.

Anti-CDS Antibodies

Antibodies to human CDS protein can be obtained using the product of a CDS expression vector or synthetic peptides derived from the CDS coding sequence coupled to a carrier (Pasnett et al., J. Biol. Chem. 263: 1728, 1988) as an antigen. The preparation of polyclonal antibodies is well-known to those of skill in the art. See, for example, Green et al., “Production of Polyclonal Antisera,” in Immunochemical Protocols (Manson, ed.), pages 1-5 (Humana Press 1992). Alternatively, a CDS antibody of the present invention may be derived as a rodent monoclonal antibody (MAb). Rodent monoclonal antibodies to specific antigens may be obtained by methods known to those skilled in the art. See, for example, Kohler and Milstein, Nature 256: 495, 1975, and Coligan et al. (eds.), Current Protocols in Immunology, 1: 2.5.1-2.6.7 (John Wiley & Sons 1991). Briefly, monoclonal antibodies can be obtained by injecting mice with a composition comprising an antigen, verifying the presence of antibody production by removing a serum sample, removing the spleen to obtain B-lymphocytes, fusing the B-lymphocytes with myeloma cells to produce hybridomas, cloning the hybridomas, selecting positive clones which produce antibodies to the antigen, culturing the clones that produce antibodies to the antigen, and isolating the antibodies from the hybridoma cultures.

MAbs can be isolated and purified from hybridoma cultures by a variety of well-established techniques. Such isolation techniques include affinity chromatography with Protein-A Sepharose, size-exclusion chromatography, and ion-exchange chromatography. See, for example, Coligan at pages 2.7.1-2.7.12 and pages 2.9.1-2.9.3. Also, see Baines et al., “Purification of Immunoglobulin G (IgG),” in Methods in Molecular Biology, 10: 79-104 Humana Press, Inc. 1992. A CDS antibody of the present invention may also be derived from a subhuman primate. General techniques for raising therapeutically useful antibodies in baboons may be found, for example, in Goldenberg et al., international patent publication No. WO 91/11465 (1991), and in Losman et al., Int. J. Cancer 46: 310, 1990.

Alternatively, a therapeutically useful CDS antibody may be derived from a “humanized” monoclonal antibody. Humanized monoclonal antibodies are produced by transferring mouse complementarity determining regions from heavy and light chain variable regions of the mouse antibody into a human antibody variable domain, and then, substituting human residues in the framework regions of the murine counterparts. The use of antibody components derived from humanized monoclonal antibodies obviates potential problems associated with the immunogenicity of murine constant regions. General techniques for cloning murine immunoglobulin variable domains are described, for example, by the publication of Orlandi et al., Proc. Nat'l. Acad. Sci. USA 86: 3833, 1989. Techniques for producing humanized MAbs are described, for example, by Jones et al., Nature 321: 522, 1986; Riechmann et al., Nature 332: 323, 1988; Verhoeyen et al., Science 239: 1534, 1988; Carter et al., Proc. Nat'l Acad. Sci. USA 89: 4285, 1992; Sandhu, Crit. Rev. Biotech. 12: 437, 1992; and Singer et al., J. Immun. 150: 2844, 1993.

As an alternative, a CDS antibody of the present invention may be derived from human antibody fragments isolated from a combinatorial immunoglobulin library. See, for example, Barbas et al., METHODS: A Companion to Methods in Enzymology 2: 119 1991, and Winter et al., Ann. Rev. Immunol. 12: 433, 1994. Cloning and expression vectors that are useful for producing a human immunoglobulin phage library can be obtained, for example, from STRATAGENE Cloning Systems (La Jolla, Calif.). In addition, a CDS antibody of the present invention may be derived from a human monoclonal antibody. Such antibodies are obtained from transgenic mice that have been “engineered” to produce specific human antibodies in response to antigenic challenge. In this technique, elements of the human heavy and light chain loci are introduced into strains of mice derived from embryonic stem cell lines that contain targeted disruptions of the endogenous heavy chain and light chain loci. The transgenic mice can synthesize human antibodies specific for human antigens, and the mice can be used to produce human antibody-secreting hybridomas. Methods for obtaining human antibodies from transgenic mice are described by Green et al., Nature Genet. 7: 13, 1994; Lonberg et al., Nature 368: 856, 1994; and Taylor et al., Int. Immun. 6.579, 1994. 

1-16. (canceled)
 17. A method for determining whether a compound is a useful pharmaceutical compound, comprising (a) contacting a first sample of a polypeptide that comprises an amino acid sequence of FIG. 8 (SEQ ID NO: 12) that has CDP-diacylglycerol synthase (CDS) activity with (i) at least one substrate for the polypeptide and (ii) at least one compound; (b) contacting a second sample of the polypeptide with the substrate but not with the compound; and (c) determining whether the CDS activity of the polypeptide of the first sample is increased or decreased in comparison to the CDS activity of the polypeptide of the second sample, wherein an increase or decrease in the CDS activity of the polypeptide of the first sample indicates that the compound modulates CDS activity and is a useful pharmaceutical compound. 